Contacts of the helix formed by residues 85 - 99 (chain C) in PDB entry 1U75
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C VAL* 3.6 27.4 - - + +
48C ARG* 3.4 29.8 - - + +
49C LEU* 3.7 29.6 - - + +
52C HIS* 3.8 24.5 - - + +
71C TYR* 3.2 23.3 + - + +
82C ASN* 3.4 33.6 + - - +
83C ALA 3.5 0.2 - - - -
84C GLY* 1.3 75.0 - - - +
86C GLN* 1.3 54.5 + - - +
87C ASN 3.0 6.1 - - - -
88C GLY* 3.0 5.5 + - - +
89C PHE* 2.9 24.6 + - - +
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TYR* 3.5 9.9 + - - +
77C PHE* 4.4 17.0 - - + +
78C ASN* 5.5 3.3 - - - -
82C ASN 4.3 6.1 - - - +
83C ALA* 3.9 9.1 - - - +
84C GLY* 3.2 26.3 - - - +
85C LEU* 1.3 78.4 - - - +
87C ASN* 1.3 64.1 + - - +
89C PHE* 3.4 10.3 + - + +
90C LYS* 3.0 41.4 + - - +
184C ASN* 5.6 0.4 + - - -
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Residues in contact with ASN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C TYR* 3.3 45.0 + - + +
42C TYR* 3.3 26.2 + - + -
84C GLY* 3.5 13.4 + - - +
86C GLN* 1.3 84.3 - - - +
88C GLY* 1.3 63.3 + - - +
90C LYS* 3.7 23.6 + - - +
91C PHE 3.4 12.5 + - - -
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 4.0 27.4 - - - +
46C LEU* 3.5 11.9 - - - +
49C LEU* 4.1 9.2 - - - -
85C LEU* 3.0 9.8 + - - -
87C ASN* 1.3 77.0 - - - +
89C PHE* 1.3 63.1 + - - +
91C PHE* 3.4 14.5 - - - +
92C LEU* 3.5 16.3 + - - +
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 4.4 5.1 - - - +
71C TYR* 4.0 18.6 - + + -
72C ARG* 4.8 9.0 - - + -
77C PHE* 3.8 33.2 - + + -
85C LEU 2.9 11.5 + - - +
86C GLN* 3.5 13.0 - - + +
87C ASN 3.2 0.2 - - - -
88C GLY* 1.3 73.0 - - - +
90C LYS* 1.3 60.3 + - + +
91C PHE 3.0 4.0 - - - -
92C LEU* 2.9 23.3 + - + +
93C GLU* 3.0 38.3 + - + +
108C PHE* 3.6 38.4 - + - -
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 5.3 0.9 + - - -
42C TYR* 5.9 1.6 - - - +
86C GLN* 3.0 33.1 + - - +
87C ASN* 4.0 27.6 + - - +
89C PHE* 1.3 75.4 - - + +
91C PHE* 1.3 58.9 + - - +
93C GLU* 3.9 27.6 - - - +
94C PRO* 3.6 14.6 - - - +
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Residues in contact with PHE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.6 34.1 - - + -
29C LYS* 3.2 69.9 - - + +
30C LEU* 3.8 13.9 - - + -
33C ASP* 4.8 0.2 - - + -
42C TYR* 3.5 45.8 - + + -
46C LEU* 3.6 29.6 - - + -
87C ASN 3.4 12.9 + - - +
88C GLY 3.4 10.1 - - - +
89C PHE 2.9 0.4 + - - -
90C LYS* 1.3 78.5 - - - +
92C LEU* 1.3 68.5 + - + +
94C PRO* 3.4 6.6 - - - +
95C ILE* 3.5 12.0 - - + +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 4.2 28.7 - - + -
46C LEU* 4.0 10.1 - - + -
49C LEU* 3.6 30.7 - - + -
88C GLY 3.5 8.5 - - - +
89C PHE* 2.9 7.5 + - + +
91C PHE* 1.3 92.3 - - + +
93C GLU* 1.3 55.6 + - - +
94C PRO 3.4 1.1 - - - -
95C ILE* 3.1 10.4 + - + +
96C HIS* 3.0 27.9 + - - +
107C LEU* 4.0 22.9 - - + +
108C PHE* 3.7 30.7 - - + -
111C GLY* 4.4 7.4 - - - -
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Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C PHE* 3.0 42.5 + - + +
90C LYS* 3.9 21.0 - - - +
92C LEU* 1.3 76.3 - - - +
94C PRO* 1.4 66.6 - - + +
96C HIS* 3.5 8.8 + - - +
97C LYS* 3.4 22.7 + - + +
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Residues in contact with PRO 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS* 3.8 21.1 - - + +
90C LYS 3.6 10.1 - - - +
91C PHE 3.4 17.5 - - - +
93C GLU* 1.4 93.7 - - + +
95C ILE* 1.3 62.5 + - + +
96C HIS 3.2 0.9 - - - -
97C LYS* 3.4 11.0 + - + +
98C GLU* 3.4 21.5 + - - +
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 4.4 2.9 - - + -
25C ALA* 4.3 19.1 - - + +
26C ILE* 3.9 44.4 - - + -
29C LYS* 4.1 16.4 - - + -
91C PHE* 3.5 33.9 - - + +
92C LEU* 3.1 13.2 + - + +
94C PRO* 1.3 77.5 - - - +
96C HIS* 1.3 57.4 + - - +
98C GLU* 3.6 5.6 + - - +
99C PHE* 3.2 40.2 + - + +
107C LEU* 4.1 15.3 - - + +
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Residues in contact with HIS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU 3.0 10.5 + - - +
93C GLU* 3.7 12.3 - - - +
94C PRO 3.2 0.4 - - - -
95C ILE* 1.3 78.0 - - - +
97C LYS* 1.3 57.4 + - - +
99C PHE 3.0 39.9 - - - +
100C PRO* 3.1 18.0 + - + +
102C ILE* 2.8 38.2 + - + +
103C SER 4.5 3.6 - - - -
104C SER* 4.4 16.2 - - - -
107C LEU* 3.8 19.2 - - + +
132C ASP* 5.5 2.5 - - - -
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C GLU* 3.4 14.2 + - + +
94C PRO* 3.6 14.4 - - + +
95C ILE 3.3 0.4 - - - -
96C HIS* 1.3 78.8 - - - +
98C GLU* 1.3 60.2 + - - +
100C PRO* 3.4 18.1 - - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 4.7 10.6 - - - +
94C PRO 3.4 12.1 + - - +
95C ILE* 3.9 7.3 - - - +
96C HIS 3.3 0.4 - - - -
97C LYS* 1.3 79.1 - - - +
99C PHE* 1.3 93.2 + - + +
100C PRO* 3.7 5.3 - - - +
101C TRP* 4.7 0.9 + - - -
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Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 3.6 40.4 - - + -
22C VAL* 3.9 16.4 - - + -
25C ALA* 3.7 24.5 - - + -
95C ILE* 3.2 28.7 + - + +
96C HIS* 3.0 11.7 - - - +
98C GLU* 1.3 107.3 - - + +
100C PRO* 1.4 63.7 - - - +
101C TRP* 3.2 40.6 + + + +
102C ILE* 3.4 25.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il